Weichen Song
Activity overview
Latest activity by Weichen Song
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Weichen Song created a post,
strange WGS GWAS result with AAF>0.99 or near 0.5
Hi all,I've been running REGENIE on 500k WGS data for a few traits and they all showed two similar strange results: Firstly, those nearly-fixed variants with AAF>0.99 showed very strong inflation (...
- Weichen Song
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Weichen Song created a post,
REGENIE step2 app seems not using multi threading
Hi all,i'm using regenie step2 from the tools library with default settings and the log file indicates that it is using 7 threads: Options in effect: --step 2 \ --bgen ukb24309_c22_b0_v1.bgen \ --p...
- Weichen Song
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Weichen Song created a post,
DRAGEN CNV and SV: is population level file avaliable?
Hi all，Currently, in the DRAGEN WGS folder, there are only individual-level gvcf available for SV and CNV, whereas population-level vcf, bgen, and plink files are available for SNV and indel. I'm w...
- Weichen Song
- 5 followers
- 3 comments
- 1 vote
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Weichen Song created a post,
about I/O limitations on the cloud when analyzing multiple vcf in parallel
Hi,I launched swiss army knife on a mem2_ssd1_v2_x2 instance and used xargs to run bcftools on two WGS vcf in parallel:process_i() { i=$1 bcftools query -i 'AC=1' -f '%CHROM\t%POS\t%ID\t%REF\t%AL...
- Weichen Song
- 2 followers
- 1 comment
- 0 votes
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Weichen Song commented,
Mike Thanks for the guidance. Now it seems that even after removing [] Hail still could not find the vcf:Error summary: HailException: arguments refer to no files: Vector(file:///mnt/project/Bulk/D...
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